Add comprehensive test suite

.codacy.yml

@@ -0,0 +1,10 @@
+engines:
+  bandit:
+    enabled: true
+    exclude_paths:
+      - tests/*
+    config:
+      ignore:
+        - B601  # generic subprocess use warning
+        - B602  # subprocess call with non-literal argument
+        - B603  # subprocess_without_shell_equals_true or similar

.github/workflows/cd.yml

@@ -32,19 +32,48 @@ jobs:
         uses: pypa/gh-action-pypi-publish@release/v1
 
   conda:
-    name: build and deploy to conda
+    name: build and deploy to conda (${{ matrix.os }})
     needs: pypi
     if: always() && needs.pypi.result == 'success'
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         os: [macOS-latest, ubuntu-latest]
         python-version: [3.11]
 
     steps:
+      - name: Debug matrix info
+        run: |
+          echo "Running on: ${{ matrix.os }}"
+          echo "Python version: ${{ matrix.python-version }}"
+          echo "Runner OS: ${{ runner.os }}"
+
       - name: Checkout source
         uses: actions/checkout@v4
 
+      - name: Wait for PyPI propagation
+        run: |
+          echo "Waiting for PyPI package to be available..."
+          PACKAGE_NAME="access-mopper"
+          VERSION=$(python -c "import versioneer; print(versioneer.get_version())")
+          echo "Looking for package: ${PACKAGE_NAME}==${VERSION}"
+
+          # Wait up to 10 minutes for the package to be available
+          for i in {1..60}; do
+            echo "Attempt $i/60: Checking PyPI availability..."
+            if pip index versions ${PACKAGE_NAME} 2>/dev/null | grep -q "${VERSION}"; then
+              echo "✅ Package ${PACKAGE_NAME}==${VERSION} is available on PyPI!"
+              break
+            fi
+            if [ $i -eq 60 ]; then
+              echo "❌ Package not found on PyPI after 10 minutes"
+              exit 1
+            fi
+            echo "Package not yet available, waiting 10 seconds..."
+            sleep 10
+          done
+
       - name: Setup conda environment
         uses: conda-incubator/setup-miniconda@v3
         with:

.github/workflows/ci.yml

@@ -6,6 +6,16 @@ on:
   push:
     branches-ignore: [main]
   workflow_dispatch:
+    inputs:
+      test_suite:
+        description: 'Which test suite to run'
+        required: true
+        default: 'unit'
+        type: choice
+        options:
+        - unit
+        - integration
+        - all
 
 jobs:
   pre-commit:
@@ -44,7 +54,20 @@ jobs:
       - name: List installed packages
         run: pixi list -e test
 
-      - name: Run tests
+      - name: Run smoke and unit tests (automatic)
+        if: github.event_name != 'workflow_dispatch'
+        run: pixi run -e test pytest tests/test_smoke.py tests/unit --cov=access_mopper --cov-report=xml
+
+      - name: Run unit tests only (manual)
+        if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_suite == 'unit'
+        run: pixi run -e test pytest tests/test_smoke.py tests/unit --cov=access_mopper --cov-report=xml
+
+      - name: Run integration tests only (manual)
+        if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_suite == 'integration'
+        run: pixi run -e test pytest tests/integration --cov=access_mopper --cov-report=xml
+
+      - name: Run all tests (manual)
+        if: github.event_name == 'workflow_dispatch' && github.event.inputs.test_suite == 'all'
         run: pixi run -e test pytest tests --cov=access_mopper --cov-report=xml
 
       - name: Upload code coverage

.github/workflows/full-tests.yml

@@ -0,0 +1,66 @@
+name: Full Test Suite
+
+on:
+  workflow_dispatch:
+    inputs:
+      test_type:
+        description: 'Type of test to run'
+        required: true
+        default: 'integration'
+        type: choice
+        options:
+        - integration
+        - e2e
+        - performance
+        - all
+
+jobs:
+  comprehensive-test:
+    name: Comprehensive Tests
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@8ca4608ef7f4daeb54f5205b20d0b7cb42f11143 # v0.8.14
+        with:
+          pixi-version: v0.39.5
+
+      - name: Create default config file
+        run: |
+          mkdir -p ~/.mopper
+          cat <<EOF > ~/.mopper/user.yml
+          creator_name: "CI Bot"
+          organisation: "ACCESS-NRI"
+          creator_email: "ci@example.com"
+          creator_url: "https://example.com"
+          EOF
+
+      - name: List installed packages
+        run: pixi list -e test
+
+      - name: Run integration tests
+        if: github.event.inputs.test_type == 'integration' || github.event.inputs.test_type == 'all'
+        run: pixi run -e test pytest tests/integration -v --tb=short
+
+      - name: Run end-to-end tests
+        if: github.event.inputs.test_type == 'e2e' || github.event.inputs.test_type == 'all'
+        run: pixi run -e test pytest tests/e2e -v --tb=short
+
+      - name: Run performance tests
+        if: github.event.inputs.test_type == 'performance' || github.event.inputs.test_type == 'all'
+        run: pixi run -e test pytest tests/performance -v --tb=short
+
+      - name: Generate coverage report (if running all tests)
+        if: github.event.inputs.test_type == 'all'
+        run: pixi run -e test pytest tests --cov=access_mopper --cov-report=xml --cov-report=html
+
+      - name: Upload coverage artifacts
+        if: github.event.inputs.test_type == 'all'
+        uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2
+        with:
+          name: coverage-report
+          path: htmlcov/

.pre-commit-config.yaml

@@ -12,9 +12,10 @@ repos:
       - id: debug-statements  # Detects print() and pdb in code
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.0  # Check the latest version
+    rev: v0.8.4  # Use a specific version
     hooks:
-      - id: ruff  # Linting
-        exclude: "^(src/access_mopper/cmor_tables|src/access_mopper/_version.py|src/access_mopper/calc_ocean.py|src/access_mopper/calc_seaice.py)$"  # Exclude files or directories
-      - id: ruff-format  # Auto-formatting
-        exclude: "^(src/access_mopper/cmor_tables|src/access_mopper/_version.py)$"
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+        exclude: "_version.py"
+      - id: ruff-format
+        exclude: "_version.py"

notebooks/Getting_started.ipynb

@@ -765,7 +765,7 @@
    "source": [
     "import dask.distributed as dask\n",
     "\n",
-    "client = dask.Client(threads_per_worker = 1)\n",
+    "client = dask.Client(threads_per_worker=1)\n",
     "client"
    ]
   },
@@ -790,6 +790,7 @@
    "source": [
     "# Here we use netcdf file from a raw ACCESS-ESM run.\n",
     "import glob\n",
+    "\n",
     "files = glob.glob(\"../../Test_data/esm1-6/atmosphere/aiihca.pa-0961*_mon.nc\")"
    ]
   },
@@ -815,15 +816,15 @@
    "outputs": [],
    "source": [
     "parent_experiment_config = {\n",
-    "        \"parent_experiment_id\": \"piControl\",\n",
-    "        \"parent_activity_id\": \"CMIP\",\n",
-    "        \"parent_source_id\": \"ACCESS-ESM1-5\",\n",
-    "        \"parent_variant_label\": \"r1i1p1f1\",\n",
-    "        \"parent_time_units\": \"days since 0001-01-01 00:00:00\",\n",
-    "        \"parent_mip_era\": \"CMIP6\",\n",
-    "        \"branch_time_in_child\": 0.0,\n",
-    "        \"branch_time_in_parent\": 54786.0,\n",
-    "        \"branch_method\": \"standard\"\n",
+    "    \"parent_experiment_id\": \"piControl\",\n",
+    "    \"parent_activity_id\": \"CMIP\",\n",
+    "    \"parent_source_id\": \"ACCESS-ESM1-5\",\n",
+    "    \"parent_variant_label\": \"r1i1p1f1\",\n",
+    "    \"parent_time_units\": \"days since 0001-01-01 00:00:00\",\n",
+    "    \"parent_mip_era\": \"CMIP6\",\n",
+    "    \"branch_time_in_child\": 0.0,\n",
+    "    \"branch_time_in_parent\": 54786.0,\n",
+    "    \"branch_method\": \"standard\",\n",
     "}"
    ]
   },
@@ -860,8 +861,8 @@
     "    variant_label=\"r1i1p1f1\",\n",
     "    grid_label=\"gn\",\n",
     "    activity_id=\"CMIP\",\n",
-    "    parent_info=parent_experiment_config # <-- This is optional, can be skipped if not needed\n",
-    "    )"
+    "    parent_info=parent_experiment_config,  # <-- This is optional, can be skipped if not needed\n",
+    ")"
    ]
   },
   {